chr9-6250546-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_033439.4(IL33):c.164A>G(p.Lys55Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000563 in 1,614,032 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033439.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL33 | NM_033439.4 | c.164A>G | p.Lys55Arg | missense_variant | 3/8 | ENST00000682010.1 | |
LOC107987046 | XR_001746614.2 | n.153-22251T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL33 | ENST00000682010.1 | c.164A>G | p.Lys55Arg | missense_variant | 3/8 | NM_033439.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000368 AC: 56AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000362 AC: 91AN: 251232Hom.: 0 AF XY: 0.000383 AC XY: 52AN XY: 135772
GnomAD4 exome AF: 0.000584 AC: 853AN: 1461680Hom.: 2 Cov.: 30 AF XY: 0.000583 AC XY: 424AN XY: 727130
GnomAD4 genome ? AF: 0.000368 AC: 56AN: 152352Hom.: 0 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.164A>G (p.K55R) alteration is located in exon 3 (coding exon 2) of the IL33 gene. This alteration results from a A to G substitution at nucleotide position 164, causing the lysine (K) at amino acid position 55 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at